scNanoHi-C: a single-cell long-read concatemer sequencing method to reveal high-order structures within individual cells

High-order three-dimensional (3D) organization of regulatory elements provide a topological basis for genes regulation, but it remains unclear that how multiple regulatory elements interact across mammalian genome in a single cell. To address this, herein, we developed scNanoHi-C, which applies Nanopore sequencing to explore genome-wide proximal high-order chromatin contacts within individual cells. Evaluation of the method suggested that scNanoHi-C reliably and effectively profiled chromosome structure and distinguished structure subtype among single cells, which could also be used to detect genomic variations including CNVs and SVs, as well as scaffold the de novo assembly of single cell genomes. Importantly, our results suggested that high-order structures were extensively existed in active transcription chromatin across the genome, and multiway interactions between enhancers and their target promoters were observed in the first time within single cells. Taken together, scNanoHi-C sparked new insights of high-order 3D genome structure at the single-cell level. single-cell 3D genomic struture profiling by scNanoHi-C